Contacts of the helix formed by residues 1040 - 1057 (chain E) in PDB entry 3F5P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1040 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039E ALA* 1.3 80.5 - - - +
1041E MET* 1.3 59.5 + - - +
1042E ARG* 3.8 10.3 + - - +
1043E GLU* 3.1 24.0 + - - +
1044E ARG 2.9 22.2 + - - -
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Residues in contact with MET1041 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
981E PHE 6.0 0.7 - - - +
982E SER* 5.2 2.7 - - - -
983E ALA* 4.4 28.7 - - + +
987E TYR* 6.2 0.4 - - + -
1039E ALA 3.4 1.0 + - - -
1040E SER* 1.3 70.3 - - - +
1042E ARG* 1.3 57.2 + - - +
1044E ARG* 2.9 10.2 + - - +
1045E ILE* 2.7 60.2 + - + +
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Residues in contact with ARG1042 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040E SER* 3.2 9.3 + - - +
1041E MET* 1.3 79.0 - - - +
1043E GLU* 1.3 64.1 + - - +
1045E ILE* 3.2 8.4 + - - +
1046E GLU* 3.0 54.2 + - - +
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Residues in contact with GLU1043 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009E SER 4.1 5.0 - - - +
1010E PHE* 3.1 54.1 - - + +
1035E VAL* 5.0 1.4 - - - +
1039E ALA* 3.8 20.2 - - - +
1040E SER* 3.1 22.5 + - - +
1042E ARG* 1.3 81.6 - - - +
1044E ARG* 1.3 58.0 + - - +
1046E GLU* 4.1 3.8 - - - +
1047E PHE* 3.0 30.0 + - - +
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Residues in contact with ARG1044 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982E SER* 5.0 7.9 - - - -
983E ALA* 4.2 21.8 - - + +
984E ALA 4.7 4.7 - - - +
1035E VAL* 4.1 24.7 + - + +
1036E ASN 2.6 35.5 + - - -
1037E GLU* 3.4 12.3 + - - +
1039E ALA* 2.5 33.0 + - - +
1040E SER 2.9 10.9 + - - +
1041E MET* 2.9 10.3 + - - +
1043E GLU* 1.3 77.8 - - - +
1045E ILE* 1.3 59.2 + - - +
1047E PHE* 3.8 6.9 - - + +
1048E LEU* 3.2 32.8 + - + +
1073E GLN 4.6 6.7 + - - -
1075E THR* 4.0 21.4 + - - +
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Residues in contact with ILE1045 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983E ALA* 3.6 19.3 - - + -
987E TYR* 3.4 45.1 - - + +
1041E MET* 2.7 38.2 + - + +
1042E ARG* 3.9 9.2 - - - +
1044E ARG* 1.3 74.9 - - - +
1046E GLU* 1.3 66.7 + - - +
1047E PHE 3.1 0.9 - - - -
1048E LEU* 3.0 5.7 + - - +
1049E ASN* 2.9 36.8 + - - +
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Residues in contact with GLU1046 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010E PHE* 4.1 17.6 - - + -
1042E ARG* 3.0 44.6 + - - +
1043E GLU* 4.2 4.0 - - - +
1045E ILE* 1.3 76.3 - - - +
1047E PHE* 1.3 58.1 + - - +
1049E ASN* 3.1 8.2 + - + +
1050E GLU* 2.9 37.1 + - - +
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Residues in contact with PHE1047 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E 741 3.4 31.1 - + - -
1010E PHE* 2.8 50.4 - + + -
1033E LYS* 3.7 10.5 - - + -
1035E VAL* 3.7 24.2 - - + -
1043E GLU 3.0 21.5 + - - +
1044E ARG* 3.8 10.5 - - + +
1046E GLU* 1.3 78.3 - - - +
1048E LEU* 1.3 76.5 + - + +
1050E GLU* 3.5 4.1 + - - +
1051E ALA* 3.4 20.5 + - + +
1075E THR* 5.3 3.4 - - + -
1077E VAL* 3.0 38.1 - - + -
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Residues in contact with LEU1048 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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983E ALA* 4.5 2.9 - - + -
984E ALA* 3.8 35.2 - - + +
987E TYR* 4.2 24.0 - - + +
988E VAL* 3.5 32.1 - - + +
1044E ARG* 3.2 25.5 + - + +
1045E ILE* 3.0 8.1 + - - +
1047E PHE* 1.3 91.8 - - + +
1049E ASN* 1.3 57.8 + - - +
1051E ALA* 3.5 10.2 + - + +
1052E SER* 3.1 22.7 + - - -
1068E VAL* 4.9 9.4 - - + -
1075E THR* 4.8 8.1 - - + -
1077E VAL* 6.2 0.4 - - + -
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Residues in contact with ASN1049 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987E TYR* 4.0 15.0 - - - +
1045E ILE* 2.9 33.6 + - - +
1046E GLU* 3.6 7.8 - - + +
1048E LEU* 1.3 75.1 - - - +
1050E GLU* 1.3 67.2 + - - +
1052E SER* 2.4 37.2 + - - -
1053E VAL* 3.6 10.0 + - - +
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Residues in contact with GLU1050 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E 741 3.5 24.3 - - + -
1009E SER* 5.1 0.5 + - - -
1010E PHE* 3.3 29.6 - - + -
1046E GLU* 2.9 17.9 + - - +
1047E PHE* 3.6 11.0 - - - +
1049E ASN* 1.3 78.7 - - - +
1051E ALA* 1.3 62.8 + - - +
1053E VAL* 3.2 15.5 + - - +
1054E MET* 3.7 17.5 + - + +
1153E ASP* 4.5 4.7 - - - +
1154E PHE* 4.7 5.3 - - - +
1155E GLY* 3.5 39.4 + - - +
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Residues in contact with ALA1051 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E 741 4.9 8.2 - - + +
1047E PHE* 3.4 12.9 + - + +
1048E LEU* 3.6 18.8 - - + +
1050E GLU* 1.3 81.2 - - - +
1052E SER* 1.3 55.9 + - - +
1053E VAL 3.1 0.2 - - - -
1054E MET* 3.0 37.0 + - - +
1055E LYS* 3.3 6.4 + - - +
1065E LEU* 3.8 22.6 - - + +
1068E VAL* 5.9 3.1 - - + -
1077E VAL* 5.1 6.1 - - + -
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Residues in contact with SER1052 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987E TYR 5.2 7.9 - - - -
1048E LEU 3.1 14.3 + - - -
1049E ASN* 2.4 42.9 + - - -
1051E ALA* 1.3 75.9 - - - +
1053E VAL* 1.3 60.6 + - - +
1055E LYS* 3.8 16.3 - - - +
1056E GLU* 4.5 3.1 + - - +
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Residues in contact with VAL1053 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049E ASN 3.7 14.6 - - - +
1050E GLU* 3.2 8.0 + - - +
1051E ALA 3.1 0.6 - - - -
1052E SER* 1.3 80.7 - - - +
1054E MET* 1.3 68.6 + - - +
1055E LYS 3.3 0.2 - - - -
1056E GLU* 3.3 18.0 + - + +
1057E PHE* 3.5 20.4 - - + -
1131E PHE* 3.6 37.7 - - + -
1154E PHE* 6.1 3.8 - - + -
1157E THR* 5.8 0.9 - - - +
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Residues in contact with MET1054 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E 741 3.5 36.3 - - + -
1050E GLU* 3.7 14.6 + - + +
1051E ALA* 3.0 24.2 + - - +
1053E VAL* 1.3 76.4 - - - +
1055E LYS* 1.3 66.2 + - - +
1057E PHE* 2.7 34.9 + - - +
1062E VAL* 6.2 0.2 - - - -
1063E VAL 5.1 3.6 - - - +
1065E LEU* 3.8 26.8 + - + +
1079E MET* 4.6 11.0 - - - -
1152E GLY 4.5 7.0 - - - +
1153E ASP* 5.7 0.2 - - - +
1154E PHE* 3.7 45.0 - - + +
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Residues in contact with LYS1055 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992E TRP* 2.9 56.9 - - + +
1051E ALA 3.3 5.4 + - - +
1052E SER* 3.8 15.9 - - - +
1054E MET* 1.3 78.8 - - - +
1056E GLU* 1.3 65.1 + - - +
1057E PHE 3.1 8.3 + - - +
1058E ASN* 5.2 2.3 - - - +
1065E LEU* 4.7 4.6 - - + +
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Residues in contact with GLU1056 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052E SER 4.5 2.1 + - - +
1053E VAL* 3.3 18.0 + - + +
1054E MET 3.0 1.0 + - - -
1055E LYS* 1.3 77.8 - - - +
1057E PHE* 1.3 68.6 + - + +
1058E ASN* 3.4 5.4 + - - +
1125E TYR* 3.4 6.8 + - - -
1129E ASN* 4.1 22.1 - - - +
1131E PHE* 3.7 22.5 - - + -
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Residues in contact with PHE1057 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053E VAL* 3.5 38.8 - - + -
1054E MET* 2.7 25.9 + - - +
1055E LYS* 3.5 5.7 - - - +
1056E GLU* 1.3 77.0 - - + +
1058E ASN* 1.3 61.1 + - - +
1059E CYS 3.7 1.6 + - - -
1062E VAL* 4.2 16.3 - - + +
1064E ARG* 4.8 14.0 + - - +
1065E LEU 5.5 0.7 + - - -
1125E TYR* 3.4 21.3 - + + -
1126E LEU* 3.5 30.7 - - + -
1129E ASN* 4.9 4.3 - - + -
1131E PHE* 3.9 30.1 - + - -
1154E PHE* 4.1 38.8 - + + -
1157E THR* 5.2 2.0 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il